EpiCompare compares different epigenetic datasets for benchmarking and quality control purposes. The report consists of three main sections:
Input peak files. Total of 2 samples:
## [1] "File1: CnR"
## [1] "File2: CnT"
This information is displayed only if summary metrics from Picard is provided. See help manual.
## Loading required package: GenomicRanges
## Loading required package: stats4
## Loading required package: BiocGenerics
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## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
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## IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
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## Filter, Find, Map, Position, Reduce, anyDuplicated, append,
## as.data.frame, basename, cbind, colnames, dirname, do.call,
## duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
## lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
## tapply, union, unique, unsplit, which.max, which.min
## Loading required package: S4Vectors
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## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:base':
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## I, expand.grid, unname
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
| Sample | Total_N | Blacklisted_Peaks (%) |
|---|---|---|
| CnR | 1 | 6.10 |
| CnT | 1670 | 5.39 |
Distribution of peak widths in each sample after removing blacklisted peaks.
Heatmap of percentage overlaps between input peak files. Hover over the heatmap for percentage values.
Heatmap of percentage overlaps between input peak files and other histone marks from ENCODE. Hover over the heatmap for percentage values.
The plot is displayed only if a reference peak file is provided and stat_plot = TRUE. Depending on the format of the reference file, the function output different plots:
ChromHMM annotates different chromatin states (ChromHMM). The annotation used were obtained from here.
ChromHMM annotation of individual peak files.
ChromHMM annotation of peaks overlapping with the reference peak file.
ChromHMM annotation of peaks non-overlapping with the reference peak file.